Main
Leonardo Collado-Torres
At the Lieber Institute for Brain Development (LIBD), I lead the R/Bioconductor-powered Team Data Science group that works on understanding the roots and signatures of disease (particularly psychiatric disorders) by zooming in across dimensions of gene activity. We achieve this by studying gene expression at all expression feature levels (genes, exons, exon-exon junctions, and un-annotated regions) and by using different gene expression measurement technologies (bulk RNA-seq, single cell/nuclei RNA-seq, and spatial transcriptomics) that provide finer biological resolution and localization of gene expression. My group works closely with collaborators from LIBD as well as from Johns Hopkins University (JHU) which reflects the cross-disciplinary approach and diversity in expertise needed to further advance our understanding of high throughout biology. I am also interested in outreach activities as member of the Bioconductor Community Advisory Board, the advisory board for rOpenSci’s Statistical Software Peer Review, and the board of the Community of Bioinformatics Software Developers in Mexico. In order to provide a supportive and stimulating research environment the team is involved in career planning, internal training opportunities, Data Science guidance sessions, the LIBD rstats club, among other initiatives.
As a quick background, I graduated from the Undergraduate Program on Genomic Sciences from the National Autonomous University of Mexico (UNAM) in 2009 and worked for two years at Winter Genomics analyzing high-throughput sequencing data. I then got a PhD in 2016 from the Department of Biostatistics at Johns Hopkins Bloomberg School of Public Health thanks to a CONACyT scholarship. There I worked with Jeff Leek and Andrew Jaffe in developing derfinder and recount. I then worked ~ 4 years as a Staff Scientist and Research Scientist in Andrew Jaffe’s lab on a variety of data analysis projects.
Every day I use R and Bioconductor, and on some days I write R packages. Occasionally I write blog posts about them and other tools. I’m a co-founder of the LIBD rstats club and the CDSB community of R and Bioconductor developers in Mexico and Latin America, just like we described at the R Consortium website.
If you want to join my team, please check the LIBD career opportunities! ^_^
Table of Contents
- Education
- Research Experience
- Industry Experience
- Funding Secured as (co-)PI
- Honors and Awards
- Publications
- Software
- Leadership and Service
- Mentoring Experience
- Teaching Experience
- Courses, Meetings, Talks, and Posters
- Languages
Education
PhD., Biostatistics
Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
2016 - 2011
- Advisors: Jeffrey T. Leek and Andrew E. Jaffe
- Thesis: Annotation-Agnostic Differential Expression and Binding Analyses.
- Description: The goal was to develop statistical methods and software that enable researchers to differentiate the sources of variation observed in RNA-seq while minimizing the dependance on known annotation. This allows researchers to correct for technological variation and study the biological variation driving their phenotype of interest. We applied these methods to further our understanding of neuropsychiatric disorders using the Lieber Institute for Brain Development human brains collection (> 1000 samples).
B.S., Genomic Sciences
National Autonomous University of Mexico (UNAM)
Cuernavaca, Morelos, Mexico
2009 - 2005
- Grade 9.71/10
- Third generation at LCG-UNAM
H.S.
ITESM Campus Cuernavaca
Cuernavaca, Morelos, Mexico
2005 - 2002
- Grade 97.8/100
- Best high school average ( 200 students): awarded ITESM system 90% scholarship for college studies, declined to join LCG-UNAM.
Research Experience
Investigator
Lieber Institute for Brain Development
Baltimore, MD, USA
2021 - 2020
- Leader of the R/Bioconductor-powered Team Data Science group at LIBD.
- Currently building a team, developing research ideas, and performing analyses for several grants.
- Applying for a formal JHU joint appointment.
- Implemented the Data Science guidance sessions system and taught internal bootcamp courses.
- Working on research projects with LIBD collaborators such as Kristen R Maynard, Keri Martinowich, Joel Kleinman, and Thomas Hyde; JHU collaborators including Stephanie Hicks, Ben Langmead, Kasper Daniel Hansen, Steven Salzberg, Fernando Goes, and Peter Zandi; external collaborators such as Mina Ryten, Nicholas Clifton, Dana Hancock, and Andrew Jaffe.
- LIBD rstats club and CDSB Mexico lead.
Research Scientist
Lieber Institute for Brain Development
Baltimore, MD, USA
2020
- Affiliated to Andrew Jaffe’s Data Science Team I.
- Official data science mentoring role at LIBD through: weekly LIBD rstats club sessions; individual 30 min guidance sessions; and occasional internal LIBD courses.
- Worked on research projects with LIBD collaborators such as Andrew E Jaffe, Kristen R Maynard, and Keri Martinowich, JHU collaborators including Stephanie Hicks, Ben Langmead, and Kasper Daniel Hansen, as well as external collaborators such as Mina Ryten and Nicholas Clifton.
- Developed recount3, biocthis, megadepth, and contributed to dasper that were included in the Bioconductor 3.12 release.
- LIBD rstats club and CDSB Mexico lead.
Staff Scientist II at Andrew Jaffe’s lab
Lieber Institute for Brain Development
Baltimore, MD, USA
2020 - 2019
- Innovation and research head at Andrew Jaffe’s Data Science Team I.
- Last author for the recount-brain project.
- Senior role in a collaborative project with Mina Ryten.
- Co-first author in the spatialLIBD project along with Kristen R Maynard. Also established a collaboration with Stephanie Hicks and Lukas M Weber.
- Presented research findings at conferences such as ASHG.
- Created or contributed to the sgejobs, libdRSE, brainflowprobes, GenomicState and spatialLIBD R packages.
- Led the LIBD rstats club and CDSB Mexico.
Staff Scientist I at Andrew Jaffe’s lab
Lieber Institute for Brain Development
Baltimore, MD, USA
2019 - 2016
- Lead or co-lead role in research projects such as BrainSEQ Phase II, recount, recountWorkflow and wgbsExprs, official mentor for two MPH students, informal mentor for members of Andrew Jaffe’s team, co-author of several research projects including recount2 and wgbsExprs.
- JHBSPH MPH advisor for Ashkaun Razmara and Amy Peterson.
- Co-authored an RNA-seq processing pipeline with Emily Burke and oversaw a collaboration with Winter Genomics that we used to process thousands of samples.
- Presented research findings at conferences such as Biology of Genomes (CSHL).
- Created new collaborations such as those with Mina Ryten from UCL and Jesus Martínez from INSP-Mexico.
- Developed the jaffelab, shinycsv, LIBDpheno, wgbsExprs, recount, recount.bwtool R packages and shiny web applications.
- Co-founded the LIBD rstats club.
- Taught at several workshops and presented research at conferences.
- Participated in several grant submissions.
- Co-founded CDSB Mexico.
Research Assistant at Jeff Leek’slab
Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
2016 - 2011
- Worked with Jeff Leek and Andrew Jaffe on improving methods such as derfinder for studying the un-annotated transcriptome and applying these methods to study the human brain transcriptome.
- Worked with Marie Diener-West as a teaching assistant for the 140.621 series of Biostatistics courses (methods and statistics) as well as for the MPH capstone program.
Bioinformatician at Enrique Morett’s Lab
IBT-UNAM
Cuernavaca, Morelos, Mexico
2011 - 2009
- Identified transcriptions start sites and transcription units in Escherichia coli and Geobacter sulfurreducens with RNA-seq data. Developed the
BacterialTranscriptionR package.
Undergrad research assistant at Guillermo Dávila’s Lab
CCG-UNAM
Cuernavaca, Morelos, Mexico
2009 - 2007
- Determined bacteriophage ecological groups by developing a method based on codon distribution of all phage sequenced genomes. Joint work with Sur Herrera-Paredes.
Undergrad research assistant at Roberto Kolter’s lab
Harvard University
Boston, MA, US
2007 - 2006
- Supervisor: Elizabeth Shank. Carried out screenings to identify bacteria that activate the production of exopolysaccharide through the activation of the gene tasA in Bacillus subtilis.
Industry Experience
I typically like creating or joining R clubs, advocate in favor of version control, find some time to keep up with developments in R, and figure out how we can work together better: from using google docs for writing papers to learning from our search history.
Data Science Division Leader
Winter Genomics
Cuernavaca, Morelos, Mexico
2011 - 2010
- Responsible for recruiting and hiring new personnel, overseeing and supervising bioinformaticians, training new employees, writing research reports, presenting reports to colleagues and clients, and organizing all scientific projects.
- Projects completed:
- integrated analysis of more than 20 RNA-seq samples for determination of transcription initiation in Escherichia coli reported in Gama-Castro et al., PMID 21051347,
- de novo assembly of four Escherichia coli strains and lead to Aguilar et al., PMID 22884033; Designed training material for new employees.
Data Scientist
Winter Genomics
Cuernavaca, Morelos, Mexico
2010 - 2009
- First scientific staff member at Winter Genomics. Developed analysis pipelines for de novo genome assembly among other uses of high-throughput sequencing data.
- Projects completed: - de novo genome assembly simulations,
- assembly and annotation of the phiVC8 bacteriophage genome.
Funding Secured as (co-)PI
R21 MH120497 from the National Institutes of Health (NIH)
An expanded framework for RNA quality correction in expression analyses in the human brain
Baltimore, MD, USA
2021 - 2020
- PI on 5R21MH120497-02 ($233,250 USD) which is for year 2/2 of an R21 that Andrew E Jaffe secured and managed during year 1 as 1R21MH120497-01.
Code for Science and Society (CS&S) Event Fund Award for CDSB
N/A
Cuernavaca, Morelos, Mexico
2021
- PI on a $18,963.40 USD grant from CS&S for organizing mini-courses and the International Bioinformatics Meeting 2021 along with the RMB and NNB-CCG-UNAM teams as described on this blog post.
R Consortium for CDSB
N/A
Cuernavaca, Morelos, Mexico
2021 - 2019
- Secured $1,000 USD yearly for organizing the CDSB summer workshops from the R Consortium R User Small Conference Fund support program.
Bioconductor Foundation of NA support for CDSB
N/A
Cuernavaca, Morelos, Mexico
2020
- Secured $1,200 USD for organizing the CDSB2020 event.
Honors and Awards
Travel awards
BioC2019, BioC2017, BioC2014, useR2013, BioC2011, From Functional Genomics to Systems Biology 2010 and BiocDevelEurope 2010.
N/A
2019 - 2010
- Taught a workshop on recount at BioC2019 and BioC2017. Gave a talk on
BacterialTranscriptionat BiocDevelEurope2010. - BioC2019 scholarship application
Publications
\(*\) indicates equal contribution, \(\dagger\) indicates corresponding author
Programmatic access to bacterial regulatory networks with regutools
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2020
- Joselyn Chávez \(*\), Carmina Barberena-Jonas \(*\), Jesus E Sotelo-Fonseca \(*\), José Alquicira-Hernández, Heladia Salgado, Leonardo Collado-Torres \(\dagger\), Alejandro Reyes \(\dagger\). Oxford Bioinformatics (2020). doi: 10.1093/bioinformatics/btaa575. bioRxiv 068551 (2020). doi: 10.1101/2020.04.29.068551
- Co-corresponding author
- Twitter summary
SynGAP isoforms differentially regulate synaptic plasticity and dendritic development
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N/A
2020
- Yoichi Araki, Ingie Hong, Timothy R Gamache, Shaowen Ju, Leonardo Collado-Torres, Joo Heon Shin, Richard L Huganir. eLife (2020) doi: 10.7554/eLife.56273. bioRxiv 922013 (2020). doi: 10.1101/2020.01.28.922013
- Supporting role: analysis
- Twitter summary
Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk
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2020
- Andrew E Jaffe \(*\) \(\dagger\), Daniel J Hoeppner \(*\), Takeshi Saito, Lou Blanpain, Joy Ukaigwe, Emily E Burke, Leonardo Collado-Torres, Ran Rato, Katsunori Tajinda, Kristen R Maynard, Matthew N Tran, Keri Martinowich, Amy Deep-Soboslay, Joo Heon Shin, Joel E Kleinman, Daniel R Weinberger, Mitsuyuki Matsumoto \(\dagger\), Thomas M Hyde \(\dagger\). Nature Neuroscience (2020). doi: 10.1038/s41593-020-0604-z
- Supporting role: analysis
- Twitter summary
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
shiny app, R/Bioconductor package, analysis code
N/A
2020
- Kristen R Maynard \(*\), Leonardo Collado-Torres \(*\), Lukas M. Weber, Cedric Uytingco, Brianna K. Barry, Stephen R. Williams, Joseph L. Catallini II, Matthew N. Tran, Zachary Besich, Madhavi Tippani, Jennifer Chew, Yifeng Yin, Joel E. Kleinman, Thomas M. Hyde, Nikhil Rao, Stephanie C. Hicks, Keri Martinowich \(\dagger\), Andrew E Jaffe \(\dagger\). bioRxiv 969931 (2020). doi: 10.1101/2020.02.28.969931
- Co-first author
- Twitter summary
Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex
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2020 - 2019
- Kira A Perzel Mandell\(^{*}\), Amanda J Price, Richard Wilton, Leonardo Collado-Torres, Ran Tao, Nicholas J Eagles, Alexander S Szalay, Thomas M Hyde, Daniel R Weinberger, Joel E Kleinman, Andrew E Jaffe\(\dagger\). Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. Epigenetics (2020). doi: 10.1080/15592294.2020.1786304. bioRxiv 823781 (2019). doi: 10.1101/823781
- Supporting role: analysis
- Twitter summary
Recounting the FANTOM CAGE–Associated Transcriptome
related code. Used data from recount2 and code from recount.bwtool
N/A
2020 - 2019
- Eddie-Luidy Imada\(^{*}\), Diego Fernando Sanchez\(^{*}\), Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Lobo-Pereira, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, Michiel JL de Hoon, Jay W Shin, Piero Carninci, Andrew E Jaffe, Jeffrey T Leek, Alexander Favorov, Gloria R Franco, Benjamin Langmead\(\dagger\), Luigi Marchionni\(\dagger\). Recounting the FANTOM Cage Associated Transcriptome. Genome Research (2020) doi: 10.1101/gr.254656 bioRxiv 659490 (2019). doi: 10.1101/659490
- Supporting role: data preparation and advice
- Twitter summary
Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information
Used data from recount2 and code from recount.bwtool
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2020 - 2019
- Sebastian Guelfi\(^{*}\), Karishma D’Sa\(^{*}\), Juan Botía\(^{*}\), Jana Vandrovcova, Regina H. Reynolds, David Zhang, Daniah Trabzuni, Leonardo Collado-Torres, Andrew Thomason, Pedro Quijada Leyton, Sarah A. Gagliano, Mike A. Nalls, International Parkinson’s Disease Genomics Consortium (IPDGC), UK Brain Expression Consortium, Kerrin S. Small, Colin Smith, Adaikalavan Ramasamy, John Hardy, Michael E. Weale\(\dagger\), Mina Ryten\(\dagger\). Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information. Nature Communications (2020) doi: 10.1038/s41467-020-14483-x. bioRxiv 591156 (2019). doi: 10.1101/591156
- Supporting role: data preparation and advice
- Twitter summary
Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders
Used data from recount2 and code from recount.bwtool
N/A
2020 - 2018
- David Zhang\(^{*}\), Sebastian Guelfi\(^{*}\), Sonia Garcia Ruiz, Beatrice Costa, Regina H Reynolds, Karishma D’Sa, Wenfei Liu, Thomas Courtin, Amy Peterson, Andrew E Jaffe, John Hardy, Juan Botia, Leonardo Collado-Torres, Mina Ryten. Incomplete annotation of OMIM genes is likely to be limiting the diagnostic yield of genetic testing, particularly for neurogenetic disorders. Science Advances (2020). doi: 10.1126/sciadv.aay8299. bioRxiv 499103 (2018). doi: 10.1101/499103
- Supervisor role, data generation, overall project advice
- Twitter summary
Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
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2020 - 2018
- Emily E Burke\(^{*}\), Joshua G Chenoweth\(^{*}\), Joo Heon Shin, Leonardo Collado-Torres, Suel Kee Kim, Nicola Micali, Yanhong Wang, Carlo Colantuoni, Richard E Straub, Daniel J Hoeppner, Huei-Ying Chen, Alana Sellers, Kamel Shibbani, Gregory R Hamersky, Marcelo Diaz Bustamante, BaDoi N Phan, William S Ulrich, Cristian Valencia, Amritha Jaishankar, Amanda J Price, Anandita Rajpurohit, Stephen A Semick, Roland Bürli, James C Barrow, Daniel J Hiler, Stephanie C Page, Keri Martinowich, Thomas M Hyde, Joel E Kleinman, Karen F Berman, José A Apud, Alan J Cross, Nick J Brandon, Daniel R Weinberger, Brady J Maher, Ronald DG McKay\(\dagger\), Andrew E Jaffe\(\dagger\). Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. Nature Communications (2020) doi: 10.1038/s41467-019-14266-z bioRxiv 380758 (2018). doi: 10.1101/380758
- Supporting role: analysis
- Twitter summary
recount-brain: a curated repository of human brain RNA-seq datasets metadata
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2019
- Ashkaun Razmara, Shannon E Ellis, Dustin J Sokolowski, Sean Davis, Michael D Wilson, Jeffrey T Leek, Andrew E Jaffe, Leonardo Collado-Torres\(\dagger\). recount-brain: a curated repository of human brain RNA-seq datasets metadata. bioRxiv 618025 (2019). doi: 10.1101/618025
- Corresponding author
- Twitter summary
Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation.
N/A
2019 - 2018
- Amanda J. Price\(^{*}\), Leonardo Collado-Torres\(^{*}\), Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E Jaffe\(\dagger\). Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation. Genome Biology 2019. doi: 10.1186/s13059-019-1805-1. bioRxiv 428391 (2018). doi: 10.1101/428391
- Co-first author
- Twitter summary and summary numbertwo
Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia
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2019 - 2018
- Leonardo Collado-Torres, Emily E Burke, Amy Peterson, JooHeon Shin, Richard E Straub, Anandita Rajpurohit, Stephen A Semick, William S Ulrich, BrainSeq Consortium, Amanda J Price, Cristian Valencia, Ran Tao, Amy Deep-Soboslay, Thomas M Hyde, Joel E Kleinman, Daniel R Weinberger\(\dagger\), Andrew E Jaffe\(\dagger\). Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia. Neuron 2019. doi: 10.1016/j.neuron.2019.05.013 bioRxiv 426213 (2018). doi: 10.1101/426213
- First-author
- Twitter summary
Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.
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N/A
2019 - 2018
- Carrie Wright\(^{*}\), Anandita Rajpurohit\(^{*}\), Emily E. Burke, Courtney Williams, Leonardo Collado-Torres, Martha Kimos, Nicholas J. Brandon, Alan J. Cross, Andrew E. Jaffe, Daniel R. Weinberger\(\dagger\), Joo Heon Shin\(\dagger\).Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. BMC Genomics (2019). doi: 10.1186/s12864-019-5870-3. bioRxiv 445437 (2018). doi: 10.1101/445437
- Supporting role
- Twitter summary
Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells.
Used data from recount2.
N/A
2019
- Anil K Madugundu, Chan Hyun Na, Raja Sekhar Nirujogi, Santosh Renuse, Kwang Pyo Kim, Kathleen H. Burns, Christopher Wilks, Ben Langmead, Shannon E. Ellis, Leonardo Collado-Torres, Marc K. Halushka, Min-Sik Kim, Akhilesh Pandey\(\dagger\). Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics 2019. doi: 10.1002/pmic.201800315
- Supporting role
- Twitter summary
Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease.
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2019 - 2018
- Stephen A Semick, Rahul A Bharadwaj, Leonardo Collado-Torres, Ran Tao, Joo Heon Shin, Amy Deep-Soboslay, James R. Weiss, Daniel R Weinberger, Thomas M Hyde, Joel E Kleinman, Andrew E Jaffe\(\dagger\), Venkata S Mattay\(\dagger\). Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease. Acta Neuropathologica 2019. doi: 10.1007/s00401-019-01966-5. bioRxiv 430603 (2018). doi: 10.1101/430603
- Supporting role: analysis
- Twitter summary
RNA-seq transcript quantification from reduced-representation data in recount2
Data available from recount2.
N/A
2018
- Fu J, Kammers K, Nellore A, Collado-Torres L, Leek JT, Taub MA. RNA-seq transcript quantification from reduced-representation data in recount2. bioRxiv 247346 (2018). doi: 10.1101/247346
- Supporting role
- Twitter summary
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome.
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2018 - 2017
- Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis MA, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE\(\dagger\), Jaffe AE\(\dagger\). Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. Molecular Psychiatry 2018. doi: 110.1038/s41380-018-0223-1. bioRxiv 236968 (2017). doi: 10.1101/236968
- Supporting role: analysis
- Twitter summary
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.
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N/A
2018 - 2017
- Jaffe AE, Straub R, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A, The BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nat. Neurosci. 2018. doi: 10.1038/s41593-018-0197-y. bioRxiv 124321 (2017). doi: 10.1101/145656
- Supporting role: analysis
- Twitter summary
Improving the value of public RNA-seq expression data by phenotype prediction.
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2018 - 2017
- Ellis SE, Collado-Torres L, Jaffe AE, Leek JT. Improving the value of public RNA-seq expression data by phenotype prediction. Nucl. Acids Res. 2018. doi: 10.1093/nar/gky102 bioRxiv 145656 (2017). doi: 10.1101/145656
- Supporting role: data preparation and advice
- Twitter summary and this tweet
Accessing over 70,000 human RNA-seq samples with Bioconductor
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N/A
2017
- Collado-Torres L\(\dagger\), Nellore A, Jaffe AE. recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]. F1000Research (2017). doi: 10.12688/f1000research.12223.1. Winning entry for the Bioinformatics Peer Prize III.
- First and corresponding author
- Twitter summary
Altered expression of histamine signaling genes in autism spectrum disorder
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N/A
2017
- Wright C, Shin JH, Rajpurohit A, Deep-Soboslay A, Collado-Torres L, Brandon NJ, Hyde TM, Kleinman JE, Jaffe AE, Cross AJ, Weinberger DR. Altered expression of histamine signaling genes in autism spectrum disorder. Translational Psychiatry 2017. doi: 10.1038/tp.2017.87
- Supporting role: visualization
- Twitter summary
Reproducible RNA-seq analysis using recount2
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N/A
2017 - 2016
- Collado-Torres L\(^{*}\), Nellore A\(^{*}\), Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis using recount2 Nature Biotechnology 2017. doi: 10.1038/nbt.3838 bioRxiv 068478 (2016). doi: 10.1101/068478
- Co-first author
- Twitter summary
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.
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N/A
2016
- Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. Genome Biology 2016. doi: 10.1186/s13059-016-1118-6. bioRxiv 038224 (2016). doi: 10.1101/038224
- Supporting role: analysis
- bioRxiv tweet
Flexible expressed region analysis for RNA-seq with derfinder.
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N/A
2016
- Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucl. Acids Res. 2016. doi: 10.1093/nar/gkw852 bioRxiv 015370 (2016). doi: 10.1101/015370
- First author
- Twitter summary
Rail-RNA: Scalable analysis of RNA-seq splicing and coverage.
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N/A
2016 - 2015
- Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B. Rail-RNA: Scalable analysis of RNA-seq splicing and coverage. Bioinformatics 2016. doi: 10.1093/bioinformatics/btw575 bioRxiv 019067 (2015). doi: 10.1101/019067
- Supporting role: analysis
- Twitter summary
regionReport: Interactive reports for region-level and feature-level genomic analyses
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N/A
2016 - 2015
- Collado-Torres L, Jaffe AE and Leek JT. regionReport: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations]. F1000Research 2016, 4:105. doi: 10.12688/f1000research.6379.2 bioRxiv 016659 (2015). doi: 10.1101/016659
- First author
- Twitter summary
Developmental regulation of human cortex transcription and its clinical relevance at single base resolution.
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N/A
2015
- Jaffe AE, Shin J, Collado-Torres L, Leek JT, et al. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat. Neurosci. 2015. doi: 10.1038/nn.3898
- Supporting role: analysis
- Twitter summary
Book chapter: Measurement, Summary, and Methodological Variation in RNA-sequencing
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N/A
2014
- Frazee AC, Collado-Torres L, Jaffe AE, Langmead B, Leek JT. Measurement, Summary, and Methodological Variation in RNA-sequencing in Statistical Analysis of Next Generation Sequencing Data, Springer, 2014, 115-128.
Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus.
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N/A
2011
- Shank EA, Klepac-Ceraj V, Collado-Torres L, Powers GE, Losick R, Kolter R. Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc. Natl. Acad. Sci. U.S.A. 2011 Nov;108(48):E1236–1243. doi: 10.1073/pnas.1103630108
- Supporting role: performed initial experiments
- Twitter summary from 2011? No such thing back then
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).
N/A
N/A
2011
- Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res. 2011 Jan;39(Database issue):D98–105. doi: 10.1093/nar/gkq1110
Software
- all_purpose: R, Ranked 220/8606 (top 2.5%) in the US and 799/72425 (top 1%) worldwide by GitHub Awards as of March 1st, 2020. Does not take into account contributions at GitHub organizations.
- statistics: Stata
- scripting: bash
- markup: LaTeX, markdown
- OS: Linux
- cluster queue: Son of Grid Engine
shiny web applications
recount3-study-explorer, spatialLIBD, recount-brain: explore recount-brain interactively. wgbsExprs: LIBD WGBS Expression explorer for the methylation and expression associations described by Price et al, 2019. shinycsv: explore a table interactively. recount: analysis-ready RNA-seq gene and exon counts datasets. MPH capstone TA office hours sign up. Simple mortgage calculator.
N/A
2021 - 2014
- Deployed links: recount3-study-explorer, spatialLIBD, recount-brain, wgbsExprs, recount, shinycsv.
Mentor role
Remotely
2020
- Mentored three CDSB alumni while they developed their first R/Bioconductor package.
Misc R packages
sgejobs: Helper functions for SGE jobs at JHPCE.
easyweb: A fast and easy way to build your own website.
libdRSE: Custom RSE objects from genomic coordinates on LIBD data.
blogdown: contributed the Insert Image and New Post addins.
recount.bwtool: Compute coverage matrices from recount quickly using bwtool.
jaffelab: commonly used functions by the Jaffe lab.
shinycsv: explore a table interactively.
enrichedRanges: identify enrichment between two sets of genomic ranges.
dots: simplify function calls.
fitbitR: visualize your FitBit data.
BacterialTranscription: identify TSSs and TUs from RNA-seq data.
N/A
2019 - 2011
Leadership and Service
Open-source software
Develop and maintain open-source biostatistical software
N/A
2021 - 2011
Peer Review
Bioinformatics, Biological Psychiatry, Biostatistics, F1000Research, Nucleic Acids Research, Scientific Reports, Statistical Applications in Genetics and Molecular Biology.
N/A
2021 - 2013
- Full details available through Publons.
Community of Bioinformatics Software Developers (CDSB in Spanish)
Co-founder and Board Member of CDSB which is a community of R and Bioconductor developers in Latin America.
N/A
2021 - 2018
JHBSPH Student rep
Student representative for the Centennial celebration of the Department of Biostatistics.
Baltimore, MD, USA
2016
JHBSPH Biostatistics Cultural Mixers
Organized Cultural Mixer events for the Department of Biostatistics with Amanda Mejia for raising cultural awareness.
Baltimore, MD, USA
2016 - 2012
Professional memberships
International Society for Computational Biology (2019), American Society of Human Genetics (2015, 2018-2021), American Statistical Association (2015-2017, 2020), ENAR student member (2014-2016), American Public Health Association (2014).
N/A
2014
JHBSPH Genomics for students
Organized the Genomics for Students group (website).
Baltimore, MD, USA
2014 - 2012
IBT-UNAM Genomics Journal Club
Organized a Genomics Journal Club at IBT-UNAM.
Cuernavaca, Morelos, Mexico
2011 - 2009
LCG-UNAM Student rep
Elected class representative for the LCG Academic Committee. Class representative for Administration Unit for Technology Information committee.
Cuernavaca, Morelos, Mexico
2009 - 2008
NNB-UNAM forum launch
Helped start the National Node of Bioinformatics (Mexico) online forum.
Cuernavaca, Morelos, Mexico
2008
Mentoring Experience
CDSB regutools project
Along with Alejandro Reyes, co-mentored Joselyn Chávez, Carmina Barberena-Jonas and Jesus Emiliano Sotelo-Fonseca for the CDSB regutools R/Bioconductor package project.
Remotely
2020 - 2019
Winter Genomics mentees
Advised and trained 13 LCG-UNAM students and alumni while working at Winter Genomics: Riveros-McKay F, Vargas-Chávez C, Dulanto-Acevedo V, Romero-Martínez S, Samaniego-Castruita J, Zepeda-Mendoza L, Vargas-Velázquez A, Noé-González M, Soto Jiménez LM, López Moyado I, Medina-Abarca H., Izquierdo-Rangel E, and Berrocal-Quezada NA.
Cuernavaca, Morelos, Mexico
2011 - 2009
LCG-UNAM mentees
Trained 3 LCG-UNAM students to take over the R/Bioconductor course: Reyes-Quiroz A, Moreno-Mayar V, and Reyes-López J.
Cuernavaca, Morelos, Mexico
2009
Teaching Experience
I am a strong believer that access to education is important, but also having mentors and sponsors and as such as I aim to be a good mentor and help others by promoting them among my peers and helping them become more visible in the research community, particularly through Twitter. Locally, I help through Data Science guidance sessions at LIBD as well as through the LIBD rstats club. My most direct way of helping Mexicans and Latino Americans is through the Community of Bioinformatics Software Developers that aims to help R/Bioconductor users become R/Bioconductor developers. I also strongly believe in giving back to your own community by passing on the knowledge you acquired at a course or conference. Historically, that’s what launched my career in R and I still learn a lot from teaching.
CDSB
CDSB at LCG-UNAM
Virtual event
2021
- Organizer and instructor for the CDSB 2021 workshop: analysis of scRNA-seq data with Bioconductor.
Introduction to RNA-seq data analysis with Bioconductor
LCG-UNAM
Virtual event
2021
- Instructor for naseq_LCG-UNAM_2021.
Analyzing scRNA-seq data with Bioconductor
LCG-EJ-UNAM
Virtual event
2020
- Instructor for OSCA_LIIGH_UNAM_2020.
CDSB
CDSB at LCG-UNAM
Cuernavaca, Morelos, Mexico
2019
- Organizer and instructor for the CDSB 2019 workshop.
Kandahar University Training
Johns Hopkins University
Dubai, UAE
2016
- Instructor for a Biostatistics and Stata workshop for Kandahar University Faculty, organized by Johns Hopkins University (website).
Statistical Methods in Public Health
Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
2016 - 2014
- Lead teaching assitant for Statistical Methods in Public Health I and II.
MPH capstone project
Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
2016 - 2014
- Teaching assitant for the MPH capstone projects. 30 min one-on-one consulting sessions (biostatistics, Stata coding).
- Develop and maintain the MPHcapstoneTA shiny application.
Statistical Methods in Public Health
Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
2016 - 2012
- Teaching assitant for Statistical Methods in Public Health I, II, III and IV.
Summer Institute
Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
2015
- Guest lecturer: Introduction to R for Public Health Researchers, Reproducible research module.
Introduction to R for Public Health Researchers
Johns Hopkins Bloomberg School of Public Health
Baltimore, MD, USA
2015
- Teaching assistant
Introduction to R and Biostatistics
LCG-UNAM
Cuernavaca, Morelos, Mexico
2012 - 2011
- Guest lecturer: Seminar 1, Introduction to Bioinformatics course
PDCB-UNAM
CCG-UNAM
Cuernavaca, Morelos, Mexico
2011
- Instructor for the course Introduction to R and Biostatistics for Biomedical Sciences Ph.D. students (website).
PDCB-UNAM
CCG-UNAM
Cuernavaca, Morelos, Mexico
2010
- Instructor for Analysis of High-Throughput Sequencing data with Bioconductor for Biomedical Sciences Ph.D. students (website).
National Bioinformatics Week
Organized by NNB-UNAM at CCG-UNAM
Cuernavaca, Morelos, Mexico
2010
- Instructor of the Introduction to Using Bioconductor for High-Throughput Sequencing Analysis practice lab at the National Bioinformatics Week.
Enrique Morett Lab
IBT-UNAM
Cuernavaca, Morelos, Mexico
2010
- Instructor for the Introduction to R and plotting with R course for Morett’s lab.
Statistical Methods and Analysis of Genomic Data
IBT-UNAM
Cuernavaca, Morelos, Mexico
2010
- Organizer and instructor (website).
Enrique Morett Lab
IBT-UNAM
Cuernavaca, Morelos, Mexico
2009
- Organizer and instructor for the course Introduction to Bioinformatics for Morett’s lab where I taught the Introduction to R and plotting with R module (website)
Seminar III: R/Bioconductor
LCG-UNAM
Cuernavaca, Morelos, Mexico
2009
- Organizer and instructor for an in-depth Bioconductor course (website)
Bioinformatics and Statistics I
LCG-UNAM
Cuernavaca, Morelos, Mexico
2008
- R and Bioconductor overview (website).
Courses, Meetings, Talks, and Posters
Most recent slides are available via speakerdeck or slideshare.
CDSB
LCG-UNAM
Virtual event
2020
JSM
N/A
Virtual event
2020
- Gave a talk on “Promoting the next wave of R/Bioconductor developers in Latin America starting in Mexico” (slides).
BioC
Dana-Farber Cancer Research Institute
Virtual event
2020
- Presented a poster on the spatialLIBD project, taught a workshop on recount2 and related projects, organized and presented at the Birds of a Feather: CDSB event, and was involved in the Community Advisory Board presentation.
useR!
Saint Louis University
Virtual event
2020
- Presented on the “Latin American Communities and Organizations” panel and wrote a blog post for the R Consortium.
The Scientist webinar
N/A
Virtual event
2020
- Presented the spatialLIBD project together with Kristen Maynard during a webinar with ~600 registered individuals that you can watch here.
rstudio::conf
N/A
San Francisco, CA, USA
2020
- Attended the JavaScript for Shiny users workshop taught by Garrick Aden-Buie.
ASHG
N/A
Houston, TX, USA
2019
- Platform talk: Regional heterogeneity in gene expression, regulation, and coherence in the frontal cortex and hippocampus across development and schizophrenia (slides).
Visitors Research Seminar
LIIGH-UNAM
Juriquilla, Qro, Mexico
2019
- Analyzing BrainSeq Phase II and generating the recount-brain resource (slides).
BioC
Rockefeller University
New York, NY, USA
2019
Biology of Genomes (BoG)
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY, USA
2019
- recount-brain: a curated repository of human brain RNA-seq datasets metadata (poster).
Staff Seminar Series
LIBD
Baltimore, MD, USA
2019
- Analyzing BrainSeq Phase II and generating the recount-brain resource (slides).
rstudio::conf
N/A
Austin, TX, USA
2019
- Attended the Building Tidy Tools workshop by Charlotte and Hadley Wickham.
Pacific Symposium on Biocomputing (PSB)
N/A
Hawaii, HI, USA
2019
Joint Genomic Meeting
Johns Hopkins University
Baltimore, MD, USA
2018
- recount-brain: a curated repository of human brain RNA-seq datasets metadata (slides).
Biological Data Science
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY, USA
2018
- Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia (poster).
ASHG
N/A
San Diego, CA, USA
2018
- Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia (poster).
CDSB
Keynote
Remotely
2018
- From learning to using to teaching to developing R (remote presentation) (slides).
SAGES
N/A
Philadelphia, PA, USA
2018
- BrainSeq Phase II: schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex (poster).
LCG-UNAM Remote Talks
LCG-UNAM
Remotely
2018
- Reproducible RNA-seq analysis with recount2 and recount-brain (slides).
SOBP
N/A
New York, NY, USA
2018
- Unique Molecular Correlates of Schizophrenia and Its Genetic Risk in the Hippocampus Compared to Frontal Cortex (slides).
Biology of Genomes (BoG)
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY, USA
2018
- BrainSeq Phase II: Schizophrenia-associated expression differences between the hippocampus and the dorsolateral prefrontal cortex (slides).
Journal Club by Dennis Lal
N/A
Remotely
2018
- recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor (slides).
IDIES
Johns Hopkins University
Baltimore, MD, USA
2017
- Getting started with recount2 and accessing it via R (poster).
JSM
N/A
Baltimore, MD, USA
2017
- Guiding principles for interactive graphics based on LIBD data science projects (slides).
Summer Institute
Johns Hopkins University
Baltimore, MD, USA
2017
- Reproducible Research and Bioinformatics (slides).
BioC
Dana-Farber Cancer Institute
Boston, MA, USA
2017
SOBP
N/A
San Diego, CA, USA
2017
- RNA-seq samples beyond the known transcriptome with derfinder and recount (slides).
Kandahar University Training
Johns Hopkins University
Dubai, UAE
2016
- Introduction at Kandahar University MPH training event (slides).
Genomeeting
INMEGEN
Mexico City, CDMX, Mexico
2016
- recount: facilitando el análisis de miles de muestras de RNA-seq (slides).
SACNAS
N/A
Long Beach, CA, USA
2016
- Using Data Science to Study Human Brain Genomic Measurements (slides).
IDIES
Johns Hopkins University
Baltimore, MD, USA
2015
- Annotation-agnostic RNA-seq differential expression analysis software (poster).
Genomics and Bioinformatics Symposium
Johns Hopkins University
Baltimore, MD, USA
2015
- Annotation-agnostic differential expression analysis (slides).
ASHG
N/A
Baltimore, MD, USA
2015
- Annotation-agnostic RNA-seq differential expression analysis software (poster).
Biostatistics Computing Club
Johns Hopkins University
Baltimore, MD, USA
2015
- Easy parallel computing with BiocParallel and HTML reports with knitrBootstrap (slides).
ENAR
N/A
Miami, FL, USA
2015
- Dissecting human brain development at high resolution using RNA-seq (slides).
Joint Genomic Meeting
Johns Hopkins University
Baltimore, MD, USA
2015
- Does mapping simulated RNA-seq reads provide information? (slides).
is3b: International Summer Symposium on Systems Biology
INMEGEN
Mexico City, CDMX, Mexico
2014
- Developmental regulation of human cortex transcription at base-pair resolution (slides).
BioC
Dana-Farber Cancer Institute
Boston, MA, USA
2014
Biostatistics Computing Club
Johns Hopkins University
Baltimore, MD, USA
2014
- Git for research (slides).
IDIES
Johns Hopkins University
Baltimore, MD, USA
2014
ENAR
N/A
Baltimore, MD, USA
2014
- Fast annotation-agnostic differential expression analysis (poster).
Delta Omega Poster Competition
Johns Hopkins University
Baltimore, MD, USA
2014
- Fast annotation-agnostic differential expression analysis (poster).
LCG-UNAM 10 year anniversary
N/A
Cuernavaca, Morelos, Mexico
2014
- Fast differential expression analysis annotation-agnostic across groups with biological replicates (slides).
Genomics and Bioinformatics Symposium
Johns Hopkins University
Baltimore, MD, USA
2013
- Fast annotation-agnostic differential expression analysis (poster).
Genomics for Students
Johns Hopkins University
Baltimore, MD, USA
2013
- Introduction to ggbio (slides).
Joint Genomic Meeting
Johns Hopkins University
Baltimore, MD, USA
2013
- Fast differential expression analysis annotation-agnostic across groups with biological replicates (slides).
Biostatistics Journal Club
Johns Hopkins University
Baltimore, MD, USA
2013
- Fast differential expression analysis annotation-agnostic across groups with biological replicates (slides).
useR!
N/A
Albacete, Spain
2013
- Differential expression analysis of RNA-seq data at base-pair resolution in multiple biological replicates (slides).
Biostatistics Department Retreat
Johns Hopkins University
Philadelphia, PA, USA
2013
- Differential expression RNA-seq analysis with a large data set from brain samples (poster).
Biostatistics Computing Club
Johns Hopkins University
Baltimore, MD, USA
2013
- Introduction to knitr (slides).
Genomics for Students
Johns Hopkins University
Baltimore, MD, USA
2013
- Introduction to High-Throughput Sequencing and RNA-seq (slides).
Genomics for Students
Johns Hopkins University
Baltimore, MD, USA
2012
- DEXSeq paper discussion (slides).
Biostatistics Computing Club
Johns Hopkins University
Baltimore, MD, USA
2012
- Introducing Git while making your academic webpage (slides).
LCG-UNAM Remote Talks
LCG-UNAM
Remotely
2011
- Introducing Biostatistics to first year LCG students (slides).
BioC
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
2011
Bioconductor Developer Meeting
EMBL
Heidelberg, Germany
2010
- BacterialTranscription: a R package to identify Transcription Start Sites and Transcription Units (slides).
From Functional Genomics to System Biology
EMBL
Heidelberg, Germany
2010
- Global Analysis of Transcription Start Sites and Transcription Units in Bacterial Genomes (poster).
National Bioinformatics Week
Organized by NNB-UNAM at CCG-UNAM
Cuernavaca, Morelos, Mexico
2010
- Introduction to using Bioconductor for High Throughput Sequencing Analysis instructor (slides).
BioC
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
2010
- Global Analysis of Transcription Start Sites and Transcription Units in Bacterial Genomes (poster).
LCG-UNAM Third Generation Symposium
CCG-UNAM
Cuernavaca, Morelos, Mexico
2009
- Bacteriophages: analyzing their diversity (slides).
BioC
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
2009
Course on Oral Communication
CCG-UNAM
Cuernavaca, Morelos, Mexico
2009
- Taught by the master Rafael Popoca.
BioC
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
2008
A Short R/Bioconductor Course
LCG-UNAM
Cuernavaca, Morelos, Mexico
2008
- Taught by James Bullard from UC Berkeley, Ph.D. student in Sandrine Dudoit’s lab at the time.
Boston Bacterial Meeting
N/A
Boston, MA, USA
2007
Department of Microbiology and Molecular Genetics Retreat
Harvard University
Boston, MA, USA
2007
Winter School in Genomics
CCG-UNAM
Cuernavaca, Morelos, Mexico
2006